Circos on cover of UCSF Magazine
The Fall 2013 issue of UCSF Magazine has my Circos illustration of personalized medicine. The human outline motif is incorporated into other design elements in the issue.
To learn how to generate the cover and variants, read the Circos Encode Cover Tutorial.
Circos on Cover of Cancer Cell
Yang et al. used network analysis approaches characterize a subtype of ovarian cancer associated with poor overall survival.
E-cadherin is a protein encoded by the CDH1 gene and is responsible for cell-cell adhesion. Yang linked the expression of E-cadherin to specific miRNAs that influenced the regulatory network singled out in this cancer subtype.
Circos deals with 8 Gb Rye Genome
Because of its large 8 Gb genome, the genomic analysis of rye has lagged behind other cereals.
To address this, Martis et al. eastablished a linear gene order model for 72% of the rye genes based on synteny information from rice, sorghum and B. distachyon.
Although it appears that six major translocations shaped the modern rye genome, highly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks.
2013 Reticulate Evolution of the Rye Genome Plant Cell
Circos Stages Mesolithic to Neolithic Transition
Bollongino et al. present evidence of a slow transition between Mesolithic hunter-gatherer groups to Neolithic farmers.
Previous theories that the foragers disappeared shortly after the arrival of farmers are at odds with palaeogenetic and isotopic data analysis from Neolithic human skeletons from the Blätterhöhle burial site in Germany. Instead of an abrupt transition, the data suggest a more complex pattern of coexistence that persisted for over 2000 years.
2013 2000 years of parallel societies in Stone Age Central Europe Science 342:479-481.
Circos in 54 million pixels
Ruddle et al. demonstrate their commodity hardware 54 million pixel data display in exploring copy number variation data.
et al.. 2013. Leveraging Wall-sized High-Resolution Displays for Comparative Genomics Analyses of Copy Number Variation. In IEEE Symposium on Biological Data Visualization, Atlanta, GA.
Circos Tracks CO2 Emissions
Kanemoto et al. report on the disturbing trend of emissions leakage, in which developing countries are displacing emissions intensive production offshore.
The report confirms previous findings that adjusting for trade, developed countries emissions have increased, not decreased. A connection is made to the kind of emissions displacement that has already occurred for air pollution, where despite aggressive legislation in major emitters total global air pollution emissions have increased.
The conclusion warns us that "if regulatory policies do not account for embodied imports, global emissions are likely to rise even if developed countries emitters enforce strong national emissions targets."
2013 International trade undermines national emission reduction targets: New evidence from air pollution Global Environmental Change
Circos Round — Lotus Sacred
The pleasing roundness of Circos is used by Ming et al. to depict the Sacred Lotus genome in the publication "Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
The Sacred lotus has religious significance in both Buddhism and Hinduism and has been used as a food and herbal medicine product in Asia for over 7,000 years. Its seeds have exceptional longevity, remaining viable for as long as 1,300 years.
The plant is known for its exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.
2013 Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol 14:R41.
6.9e11 g of oil and Circos was there
Rivers et a. describe the effects of the Deepwater Horizon blowout on the microbial blooms of petroleum-degrading bacteria.
By sequencing 66 million community transcripts, the identity of metabolically active microbes and their roles in petroleum consumption was revealed.
Plants Love Circos
Circos frequently appears in plant literature, twice on the cover of Plant Biotechnology Journal in the last year.
2013 Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes Plant biotechnology journal
2013 High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array Plant biotechnology journal
Circos Interchange Diagrams — Networks and Flow
Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.
The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).
2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280
Circos connects to the connectome
Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.
2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.
The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.
A good layman description of the work can be found at the neurosceptic blog.
2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3
Circos is the Method for Visualizing Translocations
Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.
In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.
2013 End-joining, translocations and cancer Nat Rev Cancer
Circos Paints Chromosomes of Capsella Rubella
Slotte et al. use Circos to show the genomic structures, chromosome painting and comparative genomic mapping in C. rubella, A. lyrata and A. thaliana.
Their figure illustrates how Circos is effective at showing two-way comparisons of syntenic structure. For three-way comparison, consider hive plots.
Circos on the Cover Of Journal of Pathology
The June 2013 issue of the Journal of Pathology features a pair of Circos plots on the cover. The images are from the paper by Weier et al. describing TMPRSS2 and ERG rearrangements in prostate cancer.
"TMPRSS2–ERG rearrangements occur in approximately 50% of prostate cancers and therefore represent one of the most frequently observed structural rearrangements in all cancers."
2013 Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer J Pathol 230:174-183.
Circos on the Cover Of Nature's Asian Journal of Andrology
The May 2013 Special Issue of Asian Journal of Andrology presents the outcomes from the Sixth Annual Forum on Prostate Disease (6th FPD), which was held on June 8-9, 2012 in Shanghai, China [source: nature.com]. The cover art for the issue shows a Circos plot of 90 significantly recurrent molecular alterations in prostate cancer from an analysis of 372 prostate tumors discussed in the Wyatt et al. review article.
The review summarizes the current state of understanding of prostate cancer, "including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare".
2013 The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing Asian J Androl 15:301-308.
Brain Volume in Epilepsy
Pardoe et al. find that "Sodium valproate use in epilepsy is associated with parietal lobe thinning, reduced total brain volume, and reduced white matter volume."
The cover image shows antiepileptic drug combinations in intractable focal epilepsy cases. Linked drugs were being taken concurrently by an individual. Valproate cases are highlighted in orange.
2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.
Improving miR-mRNA Predictions
Rijlaarsdam et al. describe an algorithm for improving miR-mRNA predictions.
"Algorithms predicting miR-mRNA interactions generate high numbers of possible interactions, many of which might be non-existent or irrelevant in a certain biological context. It is desirable to develop a transparent, user-friendly, unbiased tool to enrich miR-mRNA predictions."
Round is peachy
The International Peach Genome Initative has ensured that peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees.
"Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes."
No mention of fuzz is made.
Circos in Wired's Best Scientific Figures of 2012
Wired's Best Scientific Figures of 2012 includes an image created with Circos.
"Though it's long been assumed that each cell in a body contains the same basic genomic blueprint, research now suggests that genomes actually vary between cells in the same body. The figure comes from a study of copy number variation, in which stretches of DNA are repeated multiple times. In all 23 chromosomes (arrayed in radial form) researchers found copy number differences unique to each cell's physical origin (color coding). Brain cells, for example, had quite different genomes from lung cells."
2012 Extensive genetic variation in somatic human tissues Proc Natl Acad Sci U S A 109:18018-18023.
Circos swims with fish
Howe et al. report on the zebrafish reference genome.
"Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease."
Circos, Lung Cancer and Smoking
Imielinski et al. visualize mutations in the exome and genome sequences of 183 lung adenocarcinomas to reveal recurrent somatic mutations in the splicing factor gene U2AF1 and RBM10 and ARID1A, as well as EGFR and SIK2. Grouping the data revealed clusters that correlated with smoking history.
2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
For a full list of papers that used Circos, see Circos citations.